cghMCR {cghMCR} | R Documentation |
Instantiates a cghMCR object using the parameters passed.
cghMCR(segments, gapAllowed = 500, alteredLow = 0.03, alteredHigh = 0.97, spanLimit = 2e+07, recurrence = 75, thresholdType = c("quantile", "value"))
segments |
segments is a data frame extracted from the
"output" element of the object returned by segment of the
package DNAcopy or getSegments |
gapAllowed |
gapAllowed is an integer specifying low
threshold of base pair number to separate two adjacent segments,
belower which the two segments will be joined as an altered span |
alteredLow |
alteredLow is a positive number between 0 and
1 specifying the lower reshold percential value. Only segments with
values falling below this threshold are considered as altered span |
alteredHigh |
alteredHigh is a positive number between 0 and
1 specifying the upper reshold percential value. Only segments with
values falling over this threshold are considered as altered span |
recurrence |
recurrence is an integer between 1 and 100
that specifies the rate of occurrence for a gain or loss that are
observed across sample. Only gains/losses with ocurrence rate grater
than the threshold values are declared as MCRs |
spanLimit |
|
thresholdType |
thresholdType is a character string that
can be either "quantile" or "value" indicating wether
alteredLow or alteredHigh is quantial or actual value |
The function is just a constructor of the cghMCR
class
for the instantiation of a cghMCR object
An object of the cghMCR class
The function is a contribution of The Center for Applied Cancer Science of Dana-Farber Cancer Institute
Jianhua Zhang
References on S4 class
require("cghMCR") data("sampleData") segments <- getSegments(sampleData) cghmcr <- cghMCR(segments, gapAllowed = 500, alteredLow = 0.20, alteredHigh = 0.80, recurrence = 50)